[Bioc-devel] BioC 3.1 branch created

From: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie>
To: "Tiphaine Martin" <tiphaine.martin at kcl.ac.uk>
Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org>
Sent: Friday, April 17, 2015 4:30:24 AM
Subject: Re: [Bioc-devel] BioC 3.1 branch created




Hi Tiphaine,

I have followed both of your links,. and they both work for me.
Probably just a glitch in the connection ?


Hi Dan,


I have a quick question of my own,
I would like to bridge the new release branch to my Github "release"
repository, but:

    * In the dropdown of the bridge creation, release 3.0 is still
    listed. I supposed I should wait that 3.1 is listed there, to
    create the good bridge?

    * I had a GitHub repository bridged to the 3.0 release branch. Is
    it ok to use the same GitHub repository, and use "SVN wins"
    during the bridge creation? That should update GitHub with the
    new release code, right?

Many thanks,
Kevin


On 17 April 2015 at 11:43, Martin, Tiphaine <
tiphaine.martin at kcl.ac.uk > wrote:


Hi Dan,

When I try to access on my package, I have ?Internal Server Error?.
Maybe
I make a mistake somewhere.

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/
coMET
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET

Regards,
Tiphaine



On 17/04/2015 05:44, "Dan Tenenbaum" < dtenenba at fredhutch.org >
wrote:

----- Original Message -----

From: "Henrik Bengtsson" < henrik.bengtsson at ucsf.edu >
To: "Dan Tenenbaum" < dtenenba at fredhutch.org >
Cc: "bioc-devel" < bioc-devel at r-project.org >
Sent: Thursday, April 16, 2015 6:57:45 PM
Subject: Re: [Bioc-devel] BioC 3.1 branch created

On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum
< dtenenba at fredhutch.org > wrote:

The BioC 3.1 branch is now ready.

Remember, you always have access to 2 versions of your package:
the "release" and the "devel" versions.

Right now the "release" version of your package (which is not
officially released yet but will be tomorrow if
everything goes well) is in the 3.1 branch and accessible at:

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
s/<PKGNAME>

Only bug fixes and documentation improvements should go here.

As always the "devel" version of your package is at:

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
<PKGNAME>

Similarly for experiment packages, where your package is
available
in devel at

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
<PKGNAME>

The release branch of it is in:

https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs
/<PKGNAME>

Normal development of your package can now resume here.

Please let us know if you have any questions.

Was the wrong version bump done for the GitHub-SVN bridges,
because
the 'bioc-sync' commits show release version numbers and not devel
ones?!

Not the wrong version bump, but it seems like the second one didn't
come
through.

Should be sorted now. Sorry for the inconvenience.

Dan

For instance, the aroma.light GitHub repository (master branch),
which
should reflect the Bioc devel version, 'bioc-sync' made a commit
bumping the version from 1.39.5 to 1.40.0. Note that this version
is
the version for the Bioc release - not Bioc devel. I would expect
it
to be a bump to 1.41.0. Details:


https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e
426bc6c2c1b8256a9b06
(1.40.0)

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
s/affxparser/DESCRIPTION
(1.40.0)

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE
SCRIPTION
(1.41.0)

I've verified that the bridge is still to the Bioc devel SVN
(trunk/madman), because when I tweaked the Date in DESCRIPTION
(with
the wrong Version field) and pushed to GitHub, that was reflected
on
Bioc devel SVN (trunk/madman).

I see the same for aroma.light as well:


https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5d
a548110a0bf1c25d208e2
(2.4.0)

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
s/aroma.light/DESCRIPTION
(2.4.0)

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/D
ESCRIPTION
(2.5.0)

Holding back with pushes via GitHub until I resolved. Let me know
if
this is a FAQ.

Thanks,

Henrik

Thanks!

Dan